Using VisANT to Analyze Networks

Hu, Zhenjun

doi:10.1002/0471250953.bi0808s45

Cited by 15 publications

(13 citation statements)

References 45 publications

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“…Results obtained by canonical correlation analysis were validated by using an undirected weighted network constructed by R packages glasso and igraph . The network of opioid genes was visualized by using VisAnt (39). Processing of the pooled data ( n = 50 rats) resulted in the construction of the opioid genes network with strong positive correlations within each spinal area and weak correlations within the striatal halves (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…glasso cycles through the opioid genes, fitting a modified lasso regression to each gene in turn, solving the resulting individual lasso problems by coordinate descent. The estimate of sparse inverse covariance matrix was used to construct a sparse undirected weighted network by R package igraph (38), which was finally visualized by VisANT (39, 40).…”

Section: Methodsmentioning

confidence: 99%

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Intra‐ and interregional coregulation of opioid genes: broken symmetry in spinal circuits

et al. 2017

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Regulation of the formation and rewiring of neural circuits by neuropeptides may require coordinated production of these signaling molecules and their receptors that may be established at the transcriptional level. Here, we address this hypothesis by comparing absolute expression levels of opioid peptides with their receptors, the largest neuropeptide family, and by characterizing coexpression (transcriptionally coordinated) patterns of these genes. We demonstrated that expression patterns of opioid genes highly correlate within and across functionally and anatomically different areas. Opioid peptide genes, compared with their receptor genes, are transcribed at much greater absolute levels, which suggests formation of a neuropeptide cloud that covers the receptor-expressed circuits. Surprisingly, we found that both expression levels and the proportion of opioid receptors are strongly lateralized in the spinal cord, interregional coexpression patterns are side specific, and intraregional coexpression profiles are affected differently by left- and right-side unilateral body injury. We propose that opioid genes are regulated as interconnected components of the same molecular system distributed between distinct anatomic regions. The striking feature of this system is its asymmetric coexpression patterns, which suggest side-specific regulation of selective neural circuits by opioid neurohormones.-Kononenko, O., Galatenko, V., Andersson, M., Bazov, I., Watanabe, H., Zhou, X. W., Iatsyshyna, A., Mityakina, I., Yakovleva, T., Sarkisyan, D., Ponomarev, I., Krishtal, O., Marklund, N., Tonevitsky, A., Adkins, D. L., Bakalkin, G. Intra- and interregional coregulation of opioid genes: broken symmetry in spinal circuits.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Intra‐ and interregional coregulation of opioid genes: broken symmetry in spinal circuits

et al. 2017

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“…Interconnections between transcripts, defined by topological overlap measures (TOMs), of relevant modules containing FTD-genes were visualized using VisANT [ 57 ]. We only showed the strongest interconnected genes by visualizing TOMs greater than specific thresholds indicated for each module (explained in Figs.…”

Section: Methodsmentioning

confidence: 99%

Frontotemporal dementia: insights into the biological underpinnings of disease through gene co-expression network analysis

Ferrari

Forabosco

Vandrovcová

et al. 2016

Mol Neurodegeneration

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BackgroundIn frontotemporal dementia (FTD) there is a critical lack in the understanding of biological and molecular mechanisms involved in disease pathogenesis. The heterogeneous genetic features associated with FTD suggest that multiple disease-mechanisms are likely to contribute to the development of this neurodegenerative condition.We here present a systems biology approach with the scope of i) shedding light on the biological processes potentially implicated in the pathogenesis of FTD and ii) identifying novel potential risk factors for FTD. We performed a gene co-expression network analysis of microarray expression data from 101 individuals without neurodegenerative diseases to explore regional-specific co-expression patterns in the frontal and temporal cortices for 12 genes (MAPT, GRN, CHMP2B, CTSC, HLA-DRA, TMEM106B, C9orf72, VCP, UBQLN2, OPTN, TARDBP and FUS) associated with FTD and we then carried out gene set enrichment and pathway analyses, and investigated known protein-protein interactors (PPIs) of FTD-genes products.ResultsGene co-expression networks revealed that several FTD-genes (such as MAPT and GRN, CTSC and HLA-DRA, TMEM106B, and C9orf72, VCP, UBQLN2 and OPTN) were clustering in modules of relevance in the frontal and temporal cortices. Functional annotation and pathway analyses of such modules indicated enrichment for: i) DNA metabolism, i.e. transcription regulation, DNA protection and chromatin remodelling (MAPT and GRN modules); ii) immune and lysosomal processes (CTSC and HLA-DRA modules), and; iii) protein meta/catabolism (C9orf72, VCP, UBQLN2 and OPTN, and TMEM106B modules). PPI analysis supported the results of the functional annotation and pathway analyses.ConclusionsThis work further characterizes known FTD-genes and elaborates on their biological relevance to disease: not only do we indicate likely impacted regional-specific biological processes driven by FTD-genes containing modules, but also do we suggest novel potential risk factors among the FTD-genes interactors as targets for further mechanistic characterization in hypothesis driven cell biology work.Electronic supplementary materialThe online version of this article (doi:10.1186/s13024-016-0085-4) contains supplementary material, which is available to authorized users.

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“…If GS and MM are highly correlated, it means that genes are the most important elements of modules and are highly significantly associated with the trait. Finally, the interesting module network was constructed by VisANT, containing module edges with topological overlap measurement (TOM) ≥ 0.15. TOM is a parameter to calculate the interconnection between two genes.…”

Section: Methodsmentioning

confidence: 99%

Integrative Analysis of Genomics and Transcriptome Data to Identify Potential Functional Genes of BMDs in Females

Chen

Guo

et al. 2016

Journal of Bone and Mineral Research

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Osteoporosis is known to be highly heritable. However, to date, the findings from more than 20 genome-wide association studies (GWASs) have explained less than 6% of genetic risks. Studies suggest that the missing heritability data may be because of joint effects among genes. To identify novel heritability for osteoporosis, we performed a system-level study on bone mineral density (BMD) by weighted gene coexpression network analysis (WGCNA), using the largest GWAS data set for BMD in the field, Genetic Factors for Osteoporosis Consortium (GEFOS-2), and a transcriptomic gene expression data set generated from transiliac bone biopsies in women. A weighted gene coexpression network was generated for 1574 genes with GWAS nominal evidence of association (p 0.05) based on dissimilarity measurement on the expression data. Twelve distinct gene modules were identified, and four modules showed nominally significant associations with BMD (p 0.05), but only one module, the yellow module, demonstrated a good correlation between module membership (MM) and gene significance (GS), suggesting that the yellow module serves an important biological role in bone regulation. Interestingly, through characterization of module content and topology, the yellow module was found to be significantly enriched with contractile fiber part (GO:044449), which is widely recognized as having a close relationship between muscle and bone. Furthermore, detailed submodule analyses of important candidate genes (HOMER1, SPTBN1) by all edges within the yellow module implied significant enrichment of functional connections between bone and cytoskeletal protein binding. Our study yielded novel information from system genetics analyses of GWAS data jointly with transcriptomic data. The findings highlighted a module and several genes in the model as playing important roles in the regulation of bone mass in females, which may yield novel insights into the genetic basis of osteoporosis.

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Using VisANT to Analyze Networks

Cited by 15 publications

References 45 publications

Intra‐ and interregional coregulation of opioid genes: broken symmetry in spinal circuits

Intra‐ and interregional coregulation of opioid genes: broken symmetry in spinal circuits

Frontotemporal dementia: insights into the biological underpinnings of disease through gene co-expression network analysis

Integrative Analysis of Genomics and Transcriptome Data to Identify Potential Functional Genes of BMDs in Females

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